Contacts of the strand formed by residues 209 - 213 (chain A) in PDB entry 3U7U
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ARG* 2.7 29.3 + - - -
194A GLY* 5.9 0.2 - - - -
195A ARG* 5.2 4.2 + - + +
205A CYS* 4.1 9.4 - - + -
206A HIS* 3.0 29.8 + - - +
207A ARG 4.2 1.0 - - - +
208A GLU* 1.3 77.0 - - - +
210A ALA* 1.3 53.6 + - - +
212A GLY* 3.7 13.7 - - - +
213A CYS* 4.0 12.3 - - - -
217A LYS 4.3 2.9 - - - -
221A CYS* 2.0 56.1 - - + -
223A ALA 3.7 0.2 - - - -
225A MET* 3.7 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 3.8 21.8 - - + -
116A GLU* 3.4 8.3 - - + +
143A ARG* 3.7 1.6 - - - +
208A GLU 3.7 0.4 + - - -
209A CYS* 1.3 73.2 - - - +
211A GLY* 1.3 57.2 + - - +
212A GLY 3.2 9.4 + - - +
222A PHE* 3.9 0.2 - - - +
223A ALA* 2.8 42.2 + - - +
224A CYS 3.7 20.2 - - - +
225A MET* 3.9 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 3.8 13.9 - - - -
115A THR* 2.7 33.0 + - - -
116A GLU* 2.6 27.6 + - - +
184A THR* 3.5 5.4 + - - +
195A ARG* 3.3 17.6 - - - +
210A ALA* 1.3 67.9 - - - +
212A GLY* 1.3 55.4 + - - -
222A PHE* 3.9 4.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A THR* 5.3 4.5 - - - -
195A ARG* 4.4 8.0 - - - +
196A CYS 5.5 1.8 - - - -
205A CYS* 3.6 12.3 - - - -
209A CYS* 3.7 5.6 - - - +
210A ALA 3.2 4.0 + - - +
211A GLY* 1.3 78.2 - - - +
213A CYS* 1.3 63.6 + - - +
221A CYS* 3.6 2.4 - - - -
222A PHE* 2.8 37.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A CYS 5.6 0.4 - - - -
197A TYR* 3.4 33.9 - - - +
205A CYS* 2.0 49.0 - - - -
209A CYS* 4.0 7.9 - - - -
212A GLY* 1.3 73.5 - - - +
214A SER* 1.3 58.5 + - - +
215A GLY 3.1 22.7 - - - +
220A ASP 3.1 20.2 - - - +
222A PHE* 3.2 23.9 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il